fix issue when importing single end reads on bactopia tools #14

	name: nf-bactopia CI
	on:
	push:
	branches:
	- '*'
	tags-ignore:
	- '*'
	pull_request:
	branches:
	- '*'
	jobs:
	build:
	name: Build nf-bactopia
	if: "!contains(github.event.head_commit.message, '[ci skip]')"
	runs-on: ubuntu-latest
	timeout-minutes: 10
	strategy:
	fail-fast: false
	matrix:
	java_version: [17]
	nextflow_version: ['25.04']

	steps:
	- name: Environment
	run: env \| sort

	- name: Checkout
	uses: actions/checkout@v1
	with:
	fetch-depth: 1
	submodules: true

	- name: Setup Java ${{ matrix.java_version }}
	uses: actions/setup-java@v1
	with:
	java-version: ${{matrix.java_version}}
	architecture: x64
	distribution: 'temurin'

	- name: Unit tests
	run: make test
	env:
	GRADLE_OPTS: '-Dorg.gradle.daemon=false'

	- name: Setup Nextflow ${{ matrix.nextflow_version }}
	uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
	with:
	version: "${{ matrix.nextflow_version }}"

	- name: Install
	run: make install

	- name: Test
	run: nextflow run nf-bactopia-test/ -plugins nf-bactopia@1.0.0 --help

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